The fault here is not completely the schedule. If you are going to play only in division or region (East vs East) there are going to be these imbalances. The regular season imbalances will always be there too, but a little bit less because you do play everyone in their league.
For this season I would have restricted playoffs to teams in your pod. So each division would qualify a winner and a wild card. Then the 3 wild cards maybe play in some sort of double elimination series to determine the wild card.
In the future they should use strength of schedule to break ties, though that would not help this year with the division play. The big mistake with a 60-game schedule was probably not doing 12 full games within division (48 out of 60). That would have made the schedule a bit trickier with 5-team divisions, but with one interleague series going on at all times it should have been doable. Playing 12 against the other division would require a mix of 3 and 2 game series but there was a way to make it work. Or they should have just made it 63 games.
The 10 games in-division really forced them to do this 6 and 4 breakdown randomly because you simply need longer series (3 and 4 games) rather than 2 games if you are trying to lessen travel. I am guessing they erred on the side of longer series' and longer home/road swings to lessen travel. Logistics drove this, not any sense of unfairness.